We have developed an improved version of the National Institute for Environmental Studies (NIES) three-dimensional chemical transport model (TM) designed for accurate tracer transport simulations in the stratosphere, using a hybrid sigma-isentropic (σ-θ) vertical coordinate that employs both terrain-following and isentropic parts switched smoothly around the tropopause. The air-ascending rate was derived from the effective heating rate and was used to simulate vertical motion in the isentropic part of the grid (above level 350 K), which was adjusted to fit to the observed age of the air in the stratosphere. Multi-annual simulations were conducted using the NIES TM to evaluate vertical profiles and dry-air column-averaged mole fractions of CO2 and CH4. Comparisons with balloon-borne observations over Sanriku (Japan) in 2000–2007 revealed that the tracer transport simulations in the upper troposphere and lower stratosphere are performed with accuracies of ~5% for CH4 and SF6, and ~1% for CO2 compared with the observed volume-mixing ratios. The simulated column-averaged dry air mole fractions of atmospheric carbon dioxide (XCO2) and methane (XCH4) were evaluated against daily ground-based high-resolution Fourier Transform Spectrometer (FTS) observations measured at twelve sites of the Total Carbon Column Observing Network (TCCON) (Bialystok, Bremen, Darwin, Garmisch, Izaña, Lamont, Lauder, Orleans, Park Falls, Sodankylä, Tsukuba, and Wollongong) between January 2009 and January 2011. The comparison shows the model's ability to reproduce the site-dependent seasonal cycles as observed by TCCON, with correlation coefficients typically on the order 0.8–0.9 and 0.4–0.8 for XCO2 and XCH4, respectively, and mean model biases of ±0.2% and ±0.5%, excluding Sodankylä, where strong biases are found. The ability of the model to capture the tracer total column mole fractions is strongly dependent on the model's ability to reproduce seasonal variations in tracer concentrations in the planetary boundary layer (PBL). We found a marked difference in the model's ability to reproduce near-surface concentrations at sites located some distance from multiple emission sources and where high emissions play a notable role in the tracer's budget. Comparisons with aircraft observations over Surgut (West Siberia), in an area with high emissions of methane from wetlands, show contrasting model performance in the PBL and in the free troposphere. Thus, the PBL is another critical region for simulating the tracer total column mole fractions.